{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Create  LAMMPS Dump File\n",
    "1. `l_Cbpb_Cp`: Basis of the 2D lattice in the CSLp reference frame for the given (hkl) plane.\n",
    "2. `l_CRbpb_Cp`: Basis of the 2D lattice such that the basis vectors have length that is greater than rCut and the basis vectors are similar in lengths and the angle between them is close to 90. Defined in the CSLp reference frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import byxtal.tools as gbt\n",
    "import byxtal.lattice as gbl\n",
    "import pickle as pkl\n",
    "import numpy as np\n",
    "import numpy.linalg as nla\n",
    "import byxtal.misorient_fz as mfz\n",
    "import gbpy.generate_hkl_indices as ghi\n",
    "import gbpy.util_funcs_create_byxtal as uf\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "########################################################################\n",
    "l1=gbl.Lattice('Al')\n",
    "pkl_name = l1.elem_type+'_byxtal_props.pkl'\n",
    "jar = open(pkl_name, 'rb');\n",
    "\n",
    "csl_props = pkl.load(jar)\n",
    "sig_mats = csl_props['sig_mats']\n",
    "csl_mats = csl_props['csl_mats']\n",
    "dsc_mats = csl_props['dsc_mats']\n",
    "bxt_symm_props = csl_props['csl_symm_props']\n",
    "jar.close()\n",
    "########################################################################\n",
    "\n",
    "########################################################################\n",
    "pkl_name = 'bp_list_' + l1.elem_type + '.pkl'\n",
    "jar = open(pkl_name, 'rb');\n",
    "\n",
    "bp_list = pkl.load(jar)\n",
    "l_p_po = bp_list['l_p_po']\n",
    "hkl_sig_inds = bp_list['miller_inds']\n",
    "\n",
    "jar.close()\n",
    "########################################################################\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0.   , 2.025, 2.025],\n",
       "       [2.025, 0.   , 2.025],\n",
       "       [2.025, 2.025, 0.   ]])"
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_p_po"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "l1 = gbl.Lattice('Al')\n",
    "lat_par = l1.lat_params['a']\n",
    "rCut = lat_par*3\n",
    "A_cut = (rCut+lat_par)**2\n",
    "\n",
    "l_p_po = l1.l_p_po\n",
    "l_po_p = nla.inv(l_p_po)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "s1_keys = list(hkl_sig_inds.keys())\n",
    "ind1 = 0\n",
    "sig_id = s1_keys[ind1]\n",
    "hkl_inds = hkl_sig_inds[sig_id]\n",
    "l_csl_p1 = csl_mats[sig_id]\n",
    "l_csl_po1 = l_p_po.dot(l_csl_p1)\n",
    "\n",
    "tct1 = 0\n",
    "hkl1 = np.zeros((1,3), dtype='int64')\n",
    "hkl1[0,:] = hkl_inds[tct1,:]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.   , -2.025,  4.05 ],\n",
       "       [ 2.025,  2.025,  4.05 ],\n",
       "       [-2.025,  0.   ,  4.05 ]])"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_csl_po1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for i in range(len(hkl_inds)):\n",
    "#     print(i)\n",
    "#     hkl1[0,:] = hkl_inds[i,:]\n",
    "#     l_CSLbpb_CSLp = {}\n",
    "#     l_CSLbpbSig_CSLp = {}\n",
    "\n",
    "#     l_CSLbpb_CSLp_mat = ghi.compute_hkl_bpb(hkl1)\n",
    "#     l_CSLbpbSig_CSLp_mat = ghi.gen_Acut_bpb(l_CSLbpb_CSLp_mat, l_csl_po1, rCut, A_cut)\n",
    "\n",
    "#     l_Cbpb_Cp  = l_CSLbpb_CSLp_mat[0]\n",
    "#     l_CRbpb_Cp = l_CSLbpbSig_CSLp_mat[0]\n",
    "\n",
    "#     l_bp_po1 = l_csl_po1.dot(l_CRbpb_Cp)\n",
    "\n",
    "#     symm_grp_ax = bxt_symm_props[sig_id]['symm_grp_ax'];\n",
    "#     bp_symm_grp = bxt_symm_props[sig_id]['bxt_symm_grp'];\n",
    "\n",
    "#     l_p2_p1 = sig_mats[sig_id]\n",
    "#     gb_ID = uf.get_gb_uID(l1, l_bp_po1, l_p2_p1, l_p_po, bp_symm_grp, symm_grp_ax, sig_id)\n",
    "#     print(gb_ID)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [],
   "source": [
    "l_CSLbpb_CSLp = {}\n",
    "l_CSLbpbSig_CSLp = {}\n",
    "\n",
    "l_CSLbpb_CSLp_mat = ghi.compute_hkl_bpb(hkl1)\n",
    "l_CSLbpbSig_CSLp_mat = ghi.gen_Acut_bpb(l_CSLbpb_CSLp_mat, l_csl_po1, rCut, A_cut)\n",
    "\n",
    "l_Cbpb_Cp  = l_CSLbpb_CSLp_mat[0]\n",
    "l_CRbpb_Cp = l_CSLbpbSig_CSLp_mat[0]\n",
    "\n",
    "l_bp_po1 = l_csl_po1.dot(l_CRbpb_Cp)\n",
    "\n",
    "symm_grp_ax = bxt_symm_props[sig_id]['symm_grp_ax'];\n",
    "bp_symm_grp = bxt_symm_props[sig_id]['bxt_symm_grp'];\n",
    "\n",
    "l_p2_p1 = sig_mats[sig_id] \n",
    "gb_ID = uf.get_gb_uID(l1, l_bp_po1, l_p2_p1, l_p_po, bp_symm_grp, symm_grp_ax, sig_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Al_S3_1_N1_1_0_0_N2_-2_1_-2'"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gb_ID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "zCut = 25*l1.lat_params['a']\n",
    "\n",
    "threeD_upts, sim_cell2 = uf.create_half_cryst(l1, l_csl_p1, l_CRbpb_Cp, l_p_po, 'upper', zCut)\n",
    "\n",
    "l_p1_p2 = nla.inv(l_p2_p1)\n",
    "l_csl_p2 = l_p1_p2.dot(l_csl_p1)\n",
    "threeD_lpts, sim_cell1 = uf.create_half_cryst(l1, l_csl_p2, l_CRbpb_Cp, l_p_po, 'lower', zCut)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 1.43189123e+01, -3.43653896e+00,  0.00000000e+00,\n",
       "         0.00000000e+00],\n",
       "       [ 4.44089210e-16,  1.89009643e+01,  0.00000000e+00,\n",
       "         0.00000000e+00],\n",
       "       [ 0.00000000e+00,  0.00000000e+00,  2.02500000e+02,\n",
       "        -1.01250000e+02]])"
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim_cell2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([-7.,  2.,  5.])"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.matmul(np.array([-5,7,-2]), np.linalg.inv(l_p2_p1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.66666667, -0.33333333,  0.66666667],\n",
       "       [ 0.66666667,  0.66666667, -0.33333333],\n",
       "       [-0.33333333,  0.66666667,  0.66666667]])"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_p2_p1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[-1.00000000e+00,  1.11022302e-16,  1.00000000e+00],\n",
       "       [-1.11022302e-16, -1.00000000e+00,  1.00000000e+00],\n",
       "       [ 1.00000000e+00,  1.00000000e+00,  1.00000000e+00]])"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_csl_p2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "#test:leila\n",
    "l_csl_po1 = l_p_po.dot(l_csl_p1)\n",
    "l_bp_po1 = l_csl_po1.dot(l_CRbpb_Cp)\n",
    "l_po1_go = uf.compute_orientation(l_bp_po1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 1.43189123e+01, -3.43653896e+00,  0.00000000e+00],\n",
       "       [ 0.00000000e+00,  1.89009643e+01,  0.00000000e+00],\n",
       "       [ 8.88178420e-16,  8.88178420e-16,  2.02500000e+02]])"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim_cell1[0:3,0:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "gb_attr = {}\n",
    "gb_attr['cell'] = sim_cell1\n",
    "gb_attr['upts'] = threeD_upts\n",
    "gb_attr['lpts'] = threeD_lpts\n",
    "gb_attr['lattice'] = l1.elem_type\n",
    "\n",
    "pkl_name = 'gb_attr_'+gb_ID+'.pkl'\n",
    "jar = open(pkl_name,'wb')\n",
    "pkl.dump(gb_attr, jar)\n",
    "jar.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "import gbpy.lammps_dump_writer as ldw\n",
    "initial_dump = 'gb_attr_' + gb_ID + '.out'\n",
    "box_bound, dump_lamp, box_type = ldw.lammps_box(pkl_name)  # lammps creates from the pkl file\n",
    "ldw.write_lammps_dump(initial_dump, box_bound, dump_lamp, box_type)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.,  1.,  1.],\n",
       "       [-1., -1.,  1.],\n",
       "       [ 1.,  0.,  1.]])"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_csl_p1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[-1.00000000e+00,  1.11022302e-16,  1.00000000e+00],\n",
       "       [-1.11022302e-16, -1.00000000e+00,  1.00000000e+00],\n",
       "       [ 1.00000000e+00,  1.00000000e+00,  1.00000000e+00]])"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "l_csl_p2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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